rs9904288

Positions:

• chr17-48954611-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.276 in 151,956 control chromosomes in the GnomAD database, including 6,089 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6089 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48954611T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41888 AN: 151838 Hom.: 6087 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.276

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.276 AC: 41920 AN: 151956 Hom.: 6089 Cov.: 31 AF XY: 0.278 AC XY: 20624 AN XY: 74264

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.276

Alfa AF: 0.286 Hom.: 3968

Bravo AF: 0.285

Asia WGS AF: 0.198 AC: 689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9904288; hg19: chr17-47031973;